NCBI C++ ToolKit
composition_constants.h
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1 /* $Id: composition_constants.h 45264 2010-03-26 14:52:29Z satskyse $
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25 /**
26  * @file composition_constants.h
27  * Constants used in compositional score matrix adjustment
28  *
29  * @author E. Michael Gertz, Alejandro Schaffer, Yi-Kuo Yu
30  */
31 
32 
33 #ifndef __COMPOSITION_CONSTANTS__
34 #define __COMPOSITION_CONSTANTS__
35 
37 
38 #ifdef __cplusplus
39 extern "C" {
40 #endif
41 
42 /** Minimum score in a matrix */
43 #define COMPO_SCORE_MIN INT2_MIN
44 
45 /** Number of standard amino acids */
46 #define COMPO_NUM_TRUE_AA 20
47 
48 /** The largest alphabet supported by this code (the code supports 26
49  or 28 character amino acid alphabets). Used to specify the size of
50  structures that are statically allocated. */
51 #define COMPO_LARGEST_ALPHABET 28
52 
53 /* NOTE: Please keep these comments in sync with argument descriptions in
54  * CCompositionBasedStatsArgs::SetArgumentDescriptions()
55  */
56 
57 /** An collection of constants that specify all permissible
58  * modes of composition adjustment */
59 typedef enum ECompoAdjustModes {
60  /** Don't use composition based statistics */
62  /** Composition-based statistics as in NAR 29:2994-3005, 2001 */
64  /** Composition-based score adjustment as in Bioinformatics 21:902-911,
65  * 2005, conditioned on sequence properties. Cannot be applied to PSSMs. */
67  /** Composition-based score adjustment as in Bioinformatics 21:902-911,
68  * 2005, unconditionally. Cannot be applied to PSSMs. */
72 
73 
74 /** An collection of constants that specify all rules that may
75  * be used to generate a compositionally adjusted matrix. */
76 typedef enum EMatrixAdjustRule {
84 
85 
86 #ifdef __cplusplus
87 }
88 #endif
89 
90 #endif
ECompoAdjustModes
An collection of constants that specify all permissible modes of composition adjustment.
@ eCompositionBasedStats
Composition-based statistics as in NAR 29:2994-3005, 2001.
@ eCompoForceFullMatrixAdjust
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally.
@ eNoCompositionBasedStats
Don't use composition based statistics.
@ eCompositionMatrixAdjust
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence pro...
@ eNumCompoAdjustModes
EMatrixAdjustRule
An collection of constants that specify all rules that may be used to generate a compositionally adju...
@ eDontAdjustMatrix
@ eCompoScaleOldMatrix
@ eRelEntropyOldMatrixOldContext
@ eRelEntropyOldMatrixNewContext
@ eUserSpecifiedRelEntropy
@ eUnconstrainedRelEntropy
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
Modified on Sun Feb 25 03:00:23 2024 by modify_doxy.py rev. 669887